From 5d0b4fc997fc8ebe2380b54c3f9203855c7a4e9a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 26 May 2014 19:25:52 +0200
Subject: [PATCH] Moved aligners to own package

---
 .../nl/lumc/sasc/biopet/wrappers/{ => aligners}/Bwa.scala     | 4 ++--
 .../nl/lumc/sasc/biopet/wrappers/{ => aligners}/Star.scala    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)
 rename biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/{ => aligners}/Bwa.scala (93%)
 rename biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/{ => aligners}/Star.scala (97%)

diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
similarity index 93%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
rename to biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
index 1c08a4f68..905b56f32 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Bwa.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Bwa.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.wrappers.aligners
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
@@ -9,7 +9,7 @@ import scala.sys.process._
 class Bwa(val globalConfig: Config) extends CommandLineFunction {
   def this() = this(new Config(Map()))
   this.analysisName = "bwa"
-  val config: Config = globalConfig.getAsConfig("bwa")
+  val config: Config = Config.mergeConfigs(globalConfig.getAsConfig("bwa"), globalConfig)
   logger.debug("Config for " + this.analysisName + ": " + config)
 
   @Argument(doc="Bwa executeble", shortName="bwa_exe", required=false) var bwa_exe: String = config.getAsString("exe", "/usr/local/bin/bwa")
diff --git a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
similarity index 97%
rename from biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
rename to biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
index 6580013f8..0cca136cb 100644
--- a/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/Star.scala
+++ b/biopet-framework/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
@@ -1,4 +1,4 @@
-package nl.lumc.sasc.biopet.wrappers
+package nl.lumc.sasc.biopet.wrappers.aligners
 
 import nl.lumc.sasc.biopet.core._
 import org.broadinstitute.sting.queue.function.CommandLineFunction
-- 
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